Alright, so I have a faulty servo driver that was controlling the extruder, so that is one problem figured out. Thank you so much gr5, you are awesome! Is there someting that I could have done that would have caused it to stop working? Other than installing the electronics, I really didn't touch the motherboard (at least thats what I would call it) at all, and I just had it do a few bed leveling prints.
On the topic of my Ulticontroller, I have inspected the pins thoroughly and none of them seem to be bent. To go into further detail, when I plug in the Ulticontroller it doesn't light up, but when I push the button it does seem to change the light on the printhead a bit, and it causes the Ultimaker to make a sound like it is trying to do something. That isn't a very good explanation, so here is a video of it.
At the end of the clip, the sound stops, that is when I plug the USB into the computer, so the sound only happens when I have only the Ulticontroller plugged in.
I have also noticed that when the Ulticontroller is plugged in, my computer seems to have a lot more difficulty connecting to the Ultimaker. Pronterface takes a long time to connect or multiple tries, and sometimes Cura doesn't connect at all. Hopefully this provides some details to shed light on this issue.
Thanks for all the help!